1 : Peter tricked (sending her a newspaper clipping about animal killings with spirals etched in them) and then killed Laura Hale, his niece and Alpha.

2. Not all Alphas are evil.

3. Because Scott had been told that if he killed the Alpha who bit him, he's be cured of the curse of the werewolf. Derek had told Scott that he would help Scott get cured, then he broke his word and killed Peter instead...after Peter had pretty much been incapacitated.

No, I found the first season to be very straight forward and relatively easy to follow.